To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions. Gut microbes, antibiotic resistance genes (ARGs), and virulence factors genes (VFGs) were analyzed by using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug-related resistance genes and Capsule, LOS related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs. Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, Escherichia coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and Eubacterium hallii may be benificial for IBD patients and could serve as potential probiotics for IBD treatment. This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome-based therapies. This article is protected by copyright. All rights reserved.